LB-30. Origins of the Causative Agent of the German HUS Outbreak: Towards Real-time, Whole genome based Molecular Epidemiology
Session: Oral Abstract Session: Late Breaker Oral Abstracts
Saturday, October 22, 2011: 5:15 PM
Room: 156ABC
Background: The large outbreak of diarrhea with associated hemolytic uremic syndrome (HUS) in Germany in May-July 2011 was caused by an E. coli strain of serotype O104:H4 that had not previously been linked to epidemic disease.  Initial characterization of the outbreak strain suggested that it was not a typical enterohemorrhagic E. coli (EHEC) strain, which have been associated with most foodborne HUS outbreaks.  Like EHEC strains, the outbreak strain contained genes encoding Shiga toxin; however, in contrast to EHEC, the outbreak strain lacked the LEE pathogenicity island, a set of genes found in EHEC that facilitate intestinal colonization.  Instead, the outbreak strain encoded virulence-linked genes commonly found in enteroaggregative E. coli.

Methods: We used Pacific Biosciences’ single-molecule, real-time DNA sequencing technology to investigate the evolutionary origins of the outbreak strain.  The genomes of this strain, 7 additional enteroaggregative E. coli serotype O104:H4 strains, and 4 enteroaggregative strains of different serotypes were determined with ~75x coverage in ~5/hr genome.  Genomewide comparisons were carried out with these 12 genomes along with those of 40 E. coli isolates available in GenBank. 

Results: These analyses revealed that while enteroaggregative E. coli are highly diverse and spread throughout the E. coli phylogenetic tree, O104:H4 isolates, including the outbreak strain, have a conserved core genome and form a distinct clade.  However, the genome of the outbreak strain differed from those of other O104:H4 isolates in that it contained genes encoding Shiga toxin, a distinct set of additional virulence factors and resistance to antibiotics. The Shiga toxin genes were embedded in a prophage and many of the genes linked to virulence or conferring resistance to antibiotics were found on large plasmids, suggesting that horizontal transfer of genetic information by mobile genetic elements played a key role in the evolution of the E. coli O104:H4 outbreak strain. 

Conclusion: In aggregate our findings illustrate how the extraordinary capacities of emerging DNA sequencing technologies coupled with advances in bioinformatics are enabling the birth of a new field: real time whole genome-based molecular epidemiology.

Subject Category: D. Diagnostic microbiology

Matthew Waldor, MD/PhD1, David A. Rasko, PhD2, Dale Webster, PhD3, Jason W. Sahl, PhD2, Ali Bashir, PhD3, Ellen Paxinos, Ph.D.3, Robert Sebra, Ph.D.3, Chen-Shan Chin, Ph. D3, Aaron Klammer, Ph.D.3, Paul Peluso, Ph.D3, Andrew Kasarskis, Ph.D4, Susana Wang, B. S.3, John Eid, Ph.D.3, David Rank, Ph.D3, Julia Redman, B.S.5, Susan R. Steyert, PhD6, Carsten Struve, Ph.D.7, Karen A. Krogfelt, Ph.D.7, James Nataro, MD, PhD8 and Eric Schadt, PhD3, (1)Channing Laboratory, Brigham and Women’s Hospital, Harvard Medical School, and the Howard Hughes Medical Institute, Boston, MA, (2)Department of Microbiology and Immunology, University of Maryland School of Medicine Institute for Genome Sciences, Baltimore, MD, (3)Pacific Biosciences, Menlo Park, CA, (4)Genetics and Genomics, Mount Sinai, New York, NY, (5)University of Maryland School of Medicine Institute for Genome Sciences, Baltimore, MD, (6)Institute for Genome Sciences, Baltimore, MD, (7)Department of Microbiological Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark, (8)Pediatrics, University of Virginia Children's Hospital, charlottesville, VA


M. Waldor, None

D. A. Rasko, None

D. Webster, Pacific Biosciences: Employee and Shareholder, Salary

J. W. Sahl, None

A. Bashir, Pacific Biosciences: Employee and Shareholder, Salary

E. Paxinos, None

R. Sebra, None

C. S. Chin, Pacific Biosciences: Employee, Salary

A. Klammer, Pacific Biosciences: Employee and Shareholder, Salary

P. Peluso, None

A. Kasarskis, None

S. Wang, Pacific Biosciences: Employee, Salary

J. Eid, Pacific Biosciences: Employee, Salary

D. Rank, None

J. Redman, None

S. R. Steyert, None

C. Struve, None

K. A. Krogfelt, None

J. Nataro, None

E. Schadt, None

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